Greetings, I’m Haoyang Li (Lei Hou Yeung, 李昊阳)
I am currently a computer science Ph.D. student at King Abdullah University of Science and Technology (KAUST) under the supervision of Prof. Xin Gao.
I have a broad interest in developing AI models to address biological and healthcare problems. Recently, my research has focused on developing AI models for spatial biology, including spatial multi-omics, spatiotemporal omics, and pathological imaging, aimed at translational and clinical research.
Address: 4216-WS22, Level 4, Building 3, KAUST, Thuwal, KSA
Email: haoyang[dot]li[AT]kaust[dot]edu[dot]sa
Biography
Ph.D. student of computer science at KAUST (Aug 2021 – Present)
Supervised by Prof. Xin Gao
M.Sc. of computer science at Jilin Unversity (Aug 2018 – Jun 2021)
Supervised by Prof. Ying Xu
B.E. of software engineering at Jilin University (Aug 2014 – Jun 2018)
Experience
- Research intern at Stanford (Jun 2024 – Sep 2024)
- Work with by Prof. Nima Aghaeepour
- Reseach intern at Yale (Jul 2023 – Sep 2023)
- Work with by Prof. Hongyu Zhao
- Research intern at KAUST (Aug 2019 – Mar 2020)
- Work with by Prof. Xin Gao
Selected Publications
5) STP: single-cell partition for subcellular spatially resolved transcriptomics.
Haoyang Li, Qinan Hu, Zhaowen Qiu, Hui Xiong, Yuhui Hu, Xin Gao.
Nature Communications (minor revision). 2024
4) SANTO: a coarse-to-fine alignment and stitching method for spatial omics.
Haoyang Li, Yingxin Lin, Wenjia He, Wenkai Han, Xiaopeng Xu, Chencheng Xu, Elva Gao, Hongyu Zhao, Xin Gao
Nature Communications. 2024
3) A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics.
Haoyang Li*, Juexiao Zhou*, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao.
Nature communications. 2022
[Blog post] [Chinese report] [CBIRT news] [KAUST news]
Chosen as Editors’ Highlights in Nature Communications.
The 50 best papers in 'Biotechnology and methods' in Nature Communications.
2) SD2: Spatially resolved transcriptomics deconvolution through integration of spatial and dropout information.
Haoyang Li, Hanmin Li, Juexiao Zhou, Xin Gao.
Bioinformatics. 2022
1） Automatic and interpretable model for periodontitis diagnosis in panoramic radiographs.
Haoyang Li, Juexiao Zhou, Yi Zhou, Jieyu Chen, Feng Gao, Ying Xu, Xin Gao.
International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2020).
Publications
18) An AI Agent for Fully Automated Multi-omic Analyses.
Juexiao Zhou, Bin Zhang, Xiuying Chen, Haoyang Li, Xiaopeng Xu, Siyuan Chen, Xin Gao
Advanced Science. 2024
17) SANTO: a coarse-to-fine alignment and stitching method for spatial omics.
Haoyang Li, Yingxin Lin, Wenjia He, Wenkai Han, Xiaopeng Xu, Chencheng Xu, Elva Gao, Hongyu Zhao, Xin Gao
Nature Communications. 2024
16) HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer.
Xiaopeng Xu, Chencheng Xu, Wenjia He, Lesong Wei, Haoyang Li, Juexiao Zhou, Ruochi Zhang, Yu Wang, Yuanpeng Xiong, Xin Gao
Bioinformatics. 2024
15) KaryoXpert: An Accurate Chromosome Segmentation and Classification Framework for Karyotyping Analysis without Training with Manually Labeled Metaphase-Image Mask Annotations.
Siyuan Chen*, Kaichuang Zhang*, Jingdong Hu, Na Li, Ao Xu, Haoyang Li, Juexiao Zhou, Chao Huang, Yongguo Yu, and Xin Gao
Computers in Biology and Medicine. 2024
14) Personalized and privacy-preserving federated heterogeneous medical image analysis with PPPML-HMI.
Juexiao Zhou#, Longxi Zhou#, Di Wang, Xiaopeng Xu, Haoyang Li, Yuetan Chu, Wenkai Han, Xin Gao.
Computers in Biology and Medicine. 2023
13) Repetitive DNA sequence detection and its role in the human genome.
Xingyu Liao, Wufei Zhu, Juexiao Zhou, Haoyang Li, Xiaopeng Xu, Bin Zhang, Xin Gao.
Communication Biology. 2023
12) Audit to Forget: A Unified Method to Revoke Patients’ Private Data in Intelligent Healthcare.
Juexiao Zhou*, Haoyang Li*, Xingyu Liao, Bin Zhang, Wenjia He, Zhongxiao Li, Longxi Zhou, Xin Gao.
Nature Communications. 2023
11) A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics.
Haoyang Li*, Juexiao Zhou*, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao.
Nature communications. 2022
[Blog post] [Chinese report] [CBIRT news] [KAUST news]
Chosen as Editors’ Highlights in Nature Communications.
The 50 best papers in 'Biotechnology and methods' in Nature Communications.
10) Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS.
Juexiao Zhou*, Bin Zhang*, Haoyang Li, Longxi Zhou, Zhongxiao Li, Yongkang Long, Wenkai Han, Mengran Wang, Huanhuan Cui, Wei Chen, Xin Gao.
Genomics, Proteomics & Bioinformatics. 2022
9) SD2: Spatially resolved transcriptomics deconvolution through integration of spatial and dropout information.
Haoyang Li, Hanmin Li, Juexiao Zhou, Xin Gao.
Bioinformatics. 2022
8）An interpretable deep learning workflow for discovering subvisual abnormalities in CT scans of COVID-19 inpatients and survivors.
Longxi Zhou, Xianglin Meng, Yuxin Huang, Kai Kang, Juexiao Zhou, Yuetan Chu, Haoyang Li, Dexuan Xie, Jiannan Zhang, Weizhen Yang, Na Bai, Yi Zhao, Mingyan Zhao, Guohua Wang, Lawrence Carin, Xigang Xiao, Kaijiang Yu, Zhaowen Qiu, Xin Gao.
Nature machine intelligence. 2022
7） miR-596-3p suppresses brain metastasis of non-small cell lung cancer by modulating YAP1 and IL-8.
Chenlong Li, Hongshan Zheng, Hua Jin, Jinsheng Xiong, Haoyang Li, Yuxin Huang, Siqi Ai, Yingjie Wang, Tianqi Su, Guiyin Sun, Xu Xiao, Tianjiao Fu, Yujie Wang, Xin Gao, and Peng Liang.
Cell Death & Disease. 2022
6） An Interpretable Computer-Aided Diagnosis Method for Periodontitis From Panoramic Radiographs.
Haoyang Li, Juexiao Zhou, Yi Zhou, Qiang Chen, Yangyang She, Feng Gao, Ying Xu, Jieyu Chen, Xin Gao.
Frontiers in Physiology. 2021
5）A rapid, accurate and machine-agnostic segmentation and quantification method for CT-based COVID-19 diagnosis.
Longxi Zhou, Zhongxiao Li, Juexiao Zhou+, Haoyang Li+, Yupeng Chen, Yuxin Huang, Dexuan Xie, Lintao Zhao, Ming Fan, Shahrukh Hashmi, Faisal Abdelkareem, Riham Eiada, Xigang Xiao, Lihua Li, Zhaowen Qiu, Xin Gao.
IEEE transactions on medical imaging. 2020
4） Automatic and interpretable model for periodontitis diagnosis in panoramic radiographs.
Haoyang Li, Juexiao Zhou, Yi Zhou, Jieyu Chen, Feng Gao, Ying Xu, Xin Gao.
International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2020). (Oral)
3） Modern deep learning in bioinformatics.
Haoyang Li+, Shuye Tian+, Yu Li+, Qiming Fang, Renbo Tan, Yijie Pan, Chao Huang, Ying Xu, Xin Gao.
Journal of molecular cell biology. 2020
2） CaMeRe: A Novel Tool for Inference of Cancer Metabolic Reprogramming.
Haoyang Li, Juexiao Zhou, Huiyan Sun, Zhaowen Qiu, Xin Gao, Ying Xu.
Frontiers in oncology. 2020
1）Neural functions play different roles in Triple Negative Breast Cancer (TNBC) and non-TNBC.
Renbo Tan+, Haoyang Li+, Zhenyu Huang, Yi Zhou, Mingxin Tao, Xin Gao, Ying Xu.
Scientific reports. 2020
Teaching experience
- Teaching assistant, Data analytics, KAUST, Saudi Arabia, Fall 2024
- Teaching assistant, Data analytics, Ministry of Interior, Saudi Arabia, Fall 2023
- Guest lecturer, Data analytics, Saudi Aramco, Saudi Arabia, Summer 2023
- Teaching assistant, Computational biology, Jilin University, China, Spring 2019
- Teaching assistant, Bioinformatics, CCF DragonStar Summer Course, Jilin University, China, Summer 2018, 2019, 2021
Activity
- SANTO: a coarse-to-fine alignment and stitching method for spatial omics. Talk. University of Minnesota Twin Cities, 2024.
- SANTO: a coarse-to-fine alignment and stitching method for spatial omics. Talk. Jilin University, 2024.
- SANTO: a coarse-to-fine alignment and stitching method for spatial omics. Talk. Yale University, 2023.
- STP: single-cell partition for subcellular spatially resolved transcriptomics. Talk (Session: Spotlight on Young Talent). Conference on Computational Advances in Structural Biology, KAUST, 2023.
- SD2: Spatially resolved transcriptomics deconvolution through integration of spatial and dropout information. Poster. Smart-Health Student Research Symposium, KAUST, 2022.
- Deetal-Perio: DEEp denTAL Advisor for Periodontitis Diagnosis based on Two-step Segmentation of Teeth and Gingiva with Lower-dimensional Features. Poster. DigitalHealth, KAUST, 2020.
- CaMeRe: A novel tool for inference of cancer metabolic reprogramming. Poster. Advance In Artificial Intelligence, KAUST, 2019.
Academic Service
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Reviewer for Nature Biomedical Engineering, Nature Computational Science, Nature Communications, Bioinformatics, Computers in Biology and Medicine,Engineering Applications of Artificial Intelligence, ICLR 2024, ICML 2024 (AI4Science workshop), EAAI 2023, NeurIPS 2023, AAAI 2022, UAI 2022, MICCAI 2021, ICONIP 2022, SIGKDD 2022
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Editorial Board Member in Molecular & Cellular Biomechanics.
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Guest Editor Assistant in Biomedical Informatics (Special issue: spatial transcriptomics).
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Organizing Committee for International Conference on Bioinformatics (InCoB2022)
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Organizing Committee for International Workshop on Cancer Systems Biology (ICSB 2018, 2019, 2021, 2022)
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Organizer for CCF DragonStar Summer Course (2018, 2019, 2021)
Awards
- In 2021:
- Full scholarship for Ph.D. at KAUST
- Top ten graduate students of JLU (the highest honor for graduate student in JLU, 10/7000, ranked third in the ten selected students) [official report]
- Outstanding graduate student from JLU
- In 2020
- Scholarship from China Aerospace Science and Technology Corporation (CASC)
- National Scholarship of Ministry of Education
- Outstanding student of JLU
- First-class Scholarship of JLU
- Academic performance scholarship of JLU
- In 2019
- Second-class Scholarship of JLU
- Academic performance scholarship of JLU
- In 2018
- Freshman scholarship of JLU
- Academic performance scholarship of JLU
- In 2017
- Recommended for admission eligibility.
- In 2016
- Outstanding student of JLU
- Second-class scholarship of JLU
- Second prize of mathematical modeling contest of China
- In 2015
- Outstanding student of JLU
- First-class scholarship of JLU